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Whole genome sequencing of bacterial genomes - tools and applications

This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. WGS technology and applications are high on international political agenda, as the classical methods are being replaced by WGS technology and therefore bioinformatic tools are extremely important for allowing the people working in this sector to be able to analyze the data and obtain results that can be interpreted and used for different purposes. The course will give the learners a basis to understand and be acquainted with WGS applications in surveillance of bacteria including species identification, typing and characterization of antimicrobial resistance and virulence traits as well as plasmid characterization. It will also give the opportunity to learners to learn about online tools and what they can be used for through demonstrations on how to use some of these tools and exercises to be solved by learners with use of freely available WGS analysis tools .
By the end of this course you should be able to:
1. Describe the general Principles in typing of Bacteria
2. Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance
3. Apply genomic tools for sub-typing and surveillance
4. Define the concept of Next-Generation Sequencing and describe the sequencing data from NGS
5. Describe how to do de novo assembly from raw reads to contigs
6. Enumerate the methods behind the tools for species identification, MLST typing and resistance gene detection
7. Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes.
8. Describe the methods behind the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing
9. Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes.
10. Explain the concept and be able to use the integrated bacterial analysis pipeline for batch analysis and typing of genomic data
11. Demonstrate how to construct phylogenetic tree based on SNPs
12. Apply the phylogenetic tool to construct phylogenetic trees and explain the relatedness of bacterial or pathogen strains
13. Describe how to create your own sequence database
14. Utilize the MyDbFinder tool to detect genetic markers of interest from whole genome sequencing

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What people are saying

We analyzed reviews for this course to surface learners' thoughts about it

whole genome sequencing in 9 reviews

Whole genome sequencing is a wide area of science that combines knowledge in Biology, Computer Science and Mathematics.

This is an excellent course to get started on the topic of whole genome sequencing.

After completing the course I had opportunity to work with Whole Genome Sequencing of isolate from Salmonella samples .

This course enabled the learner to get novel insights into the application of whole genome sequencing of bacterial genomes, demonstrated the analysis tools/pipline available online for multiple analyzes.

When I started this online course, I had loophole in how I should handle my sequences for whole genome sequencing.

But now, I'm grasp the full understanding behind whole genome sequencing and have changed my project outline since then.

i must confess, i will recommend the course for any student wanting to learn Whole Genome Sequencing Excellent introductory course - understanding the theory and application of the knowledge were both covered.

I will highly recommend this course to microbiology students especially the ones without prior knowledge of basic bioinformatics for epidemiological study of bacterial infections This is a very interesting course, it's practical and simple to follow and I've learned a lot about whole genome sequencing and its techniques.

very interesting course in 4 reviews

It is a very interesting course and I recommend it.

A very interesting course, well designed specially for beginners which needs a strong background before going into more detail stuffs EXCELLENT COURSE GOOD FOR ANY ONE WHO HAS A BASIC KNOWLEDGE ON GENETICS The contents of the course were really very good and with loads of knowledge.

A very interesting course.

so much in 4 reviews

Thank you so much for the professors as they shared the knowledge and experience with me.

Thank You so much Mam for these courses.

I learnt so much from the course.

Cheers Excellent, had so much fun doing the course.

different tools in 4 reviews

Learn the basics of WGS and how to use different tools for data analysis: species identification, plasmid search, resistance genes search, serotyping... All with a good structure and very well explained.

Although it partly feels like pure advertisement of the tools and the videos describing usage of the different tools are very repetitive, overall the course gives a good insight.

I lerned how to use different tools to understant a DNA information, with a lot of practical exercises.

However, anyone can learn the biology behind these methods It is totally beneficial course for those who are working in epidemiology, however; I was expected to learn different tools for species and microbial communities identification.

well as in 3 reviews

Thank you great team from DTU, I get to understand NGS via your detailed explanation and useful demonstration as well as example exercise.

I am sorry if "Discussion Forum" is already there and I have ignored that.Thanks You very much,Gourab Das This course provides a first hand view of whole genome sequencing (at the contig level anyway) as well as providing the concepts and tools for characterizing and typing bacteria and their associated plasmids.

you have given such clarity of vision and progressive motion of what is the future of Medical Pathology Diagnostics and all supplanted fields of Microbiology and Genomics, as well as Metagenomics.

very easy in 3 reviews

The tools mentioned are very easy to use and applications of the tools in the real world is very interesting.

The module was easy to follow and the class exercises made it very easy to understand.

very easy and interactive Madam/Sir,I am a Computer Science Engineer, I am doing research in University of Calcutta in Machine Learning.

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